Malaria Likelihood Prediction By Effectively Surveying Households Using Deep Reinforcement Learning

We build a deep reinforcement learning (RL) agent that can predict the likelihood of an individual testing positive for malaria by asking questions about their household. The RL agent learns to determine which survey question to ask next and when to stop to make a prediction about their likelihood of malaria based on their responses hitherto. The agent incurs a small penalty for each question asked, and a large reward/penalty for making the correct/wrong prediction; it thus has to learn to balance the length of the survey with the accuracy of its final predictions. Our RL agent is a Deep Q-network that learns a policy directly from the responses to the questions, with an action defined for each possible survey question and for each possible prediction class. We focus on Kenya, where malaria is a massive health burden, and train the RL agent on a dataset of 6481 households from the Kenya Malaria Indicator Survey 2015. To investigate the importance of having survey questions be adaptive to responses, we compare our RL agent to a supervised learning (SL) baseline that fixes its set of survey questions a priori. We evaluate on prediction accuracy and on the number of survey questions asked on a holdout set and find that the RL agent is able to predict with 80% accuracy, using only 2.5 questions on average. In addition, the RL agent learns to survey adaptively to responses and is able to match the SL baseline in prediction accuracy while significantly reducing survey length.Comment: Accepted at NIPS 2017 Workshop on Machine Learning for Health (NIPS 2017 ML4H

Know What You Don't Know: Unanswerable Questions for SQuAD

Extractive reading comprehension systems can often locate the correct answer to a question in a context document, but they also tend to make unreliable guesses on questions for which the correct answer is not stated in the context. Existing datasets either focus exclusively on answerable questions, or use automatically generated unanswerable questions that are easy to identify. To address these weaknesses, we present SQuAD 2.0, the latest version of the Stanford Question Answering Dataset (SQuAD). SQuAD 2.0 combines existing SQuAD data with over 50,000 unanswerable questions written adversarially by crowdworkers to look similar to answerable ones. To do well on SQuAD 2.0, systems must not only answer questions when possible, but also determine when no answer is supported by the paragraph and abstain from answering. SQuAD 2.0 is a challenging natural language understanding task for existing models: a strong neural system that gets 86% F1 on SQuAD 1.1 achieves only 66% F1 on SQuAD 2.0.Comment: ACL 201

SQuAD: 100,000+ Questions for Machine Comprehension of Text

We present the Stanford Question Answering Dataset (SQuAD), a new reading comprehension dataset consisting of 100,000+ questions posed by crowdworkers on a set of Wikipedia articles, where the answer to each question is a segment of text from the corresponding reading passage. We analyze the dataset to understand the types of reasoning required to answer the questions, leaning heavily on dependency and constituency trees. We build a strong logistic regression model, which achieves an F1 score of 51.0%, a significant improvement over a simple baseline (20%). However, human performance (86.8%) is much higher, indicating that the dataset presents a good challenge problem for future research. The dataset is freely available at https://stanford-qa.comComment: To appear in Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing (EMNLP

Cardiologist-Level Arrhythmia Detection with Convolutional Neural Networks

We develop an algorithm which exceeds the performance of board certified cardiologists in detecting a wide range of heart arrhythmias from electrocardiograms recorded with a single-lead wearable monitor. We build a dataset with more than 500 times the number of unique patients than previously studied corpora. On this dataset, we train a 34-layer convolutional neural network which maps a sequence of ECG samples to a sequence of rhythm classes. Committees of board-certified cardiologists annotate a gold standard test set on which we compare the performance of our model to that of 6 other individual cardiologists. We exceed the average cardiologist performance in both recall (sensitivity) and precision (positive predictive value)

CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT

The extraction of labels from radiology text reports enables large-scale training of medical imaging models. Existing approaches to report labeling typically rely either on sophisticated feature engineering based on medical domain knowledge or manual annotations by experts. In this work, we introduce a BERT-based approach to medical image report labeling that exploits both the scale of available rule-based systems and the quality of expert annotations. We demonstrate superior performance of a biomedically pretrained BERT model first trained on annotations of a rule-based labeler and then finetuned on a small set of expert annotations augmented with automated backtranslation. We find that our final model, CheXbert, is able to outperform the previous best rules-based labeler with statistical significance, setting a new SOTA for report labeling on one of the largest datasets of chest x-rays

Effect of Radiology Report Labeler Quality on Deep Learning Models for Chest X-Ray Interpretation

Although deep learning models for chest X-ray interpretation are commonly trained on labels generated by automatic radiology report labelers, the impact of improvements in report labeling on the performance of chest X-ray classification models has not been systematically investigated. We first compare the CheXpert, CheXbert, and VisualCheXbert labelers on the task of extracting accurate chest X-ray image labels from radiology reports, reporting that the VisualCheXbert labeler outperforms the CheXpert and CheXbert labelers. Next, after training image classification models using labels generated from the different radiology report labelers on one of the largest datasets of chest X-rays, we show that an image classification model trained on labels from the VisualCheXbert labeler outperforms image classification models trained on labels from the CheXpert and CheXbert labelers. Our work suggests that recent improvements in radiology report labeling can translate to the development of higher performing chest X-ray classification models.Comment: In Neural Information Processing Systems (NeurIPS) Workshop on Data-Centric AI (DCAI

MoCo-CXR: MoCo Pretraining Improves Representation and Transferability of Chest X-ray Models

Contrastive learning is a form of self-supervision that can leverage unlabeled data to produce pretrained models. While contrastive learning has demonstrated promising results on natural image classification tasks, its application to medical imaging tasks like chest X-ray interpretation has been limited. In this work, we propose MoCo-CXR, which is an adaptation of the contrastive learning method Momentum Contrast (MoCo), to produce models with better representations and initializations for the detection of pathologies in chest X-rays. In detecting pleural effusion, we find that linear models trained on MoCo-CXR-pretrained representations outperform those without MoCo-CXR-pretrained representations, indicating that MoCo-CXR-pretrained representations are of higher-quality. End-to-end fine-tuning experiments reveal that a model initialized via MoCo-CXR-pretraining outperforms its non-MoCo-CXR-pretrained counterpart. We find that MoCo-CXR-pretraining provides the most benefit with limited labeled training data. Finally, we demonstrate similar results on a target Tuberculosis dataset unseen during pretraining, indicating that MoCo-CXR-pretraining endows models with representations and transferability that can be applied across chest X-ray datasets and tasks

Driverseat: Crowdstrapping Learning Tasks for Autonomous Driving

While emerging deep-learning systems have outclassed knowledge-based approaches in many tasks, their application to detection tasks for autonomous technologies remains an open field for scientific exploration. Broadly, there are two major developmental bottlenecks: the unavailability of comprehensively labeled datasets and of expressive evaluation strategies. Approaches for labeling datasets have relied on intensive hand-engineering, and strategies for evaluating learning systems have been unable to identify failure-case scenarios. Human intelligence offers an untapped approach for breaking through these bottlenecks. This paper introduces Driverseat, a technology for embedding crowds around learning systems for autonomous driving. Driverseat utilizes crowd contributions for (a) collecting complex 3D labels and (b) tagging diverse scenarios for ready evaluation of learning systems. We demonstrate how Driverseat can crowdstrap a convolutional neural network on the lane-detection task. More generally, crowdstrapping introduces a valuable paradigm for any technology that can benefit from leveraging the powerful combination of human and computer intelligence

CheXseg: Combining Expert Annotations with DNN-generated Saliency Maps for X-ray Segmentation

Medical image segmentation models are typically supervised by expert annotations at the pixel-level, which can be expensive to acquire. In this work, we propose a method that combines the high quality of pixel-level expert annotations with the scale of coarse DNN-generated saliency maps for training multi-label semantic segmentation models. We demonstrate the application of our semi-supervised method, which we call CheXseg, on multi-label chest x-ray interpretation. We find that CheXseg improves upon the performance (mIoU) of fully-supervised methods that use only pixel-level expert annotations by 13.4% and weakly-supervised methods that use only DNN-generated saliency maps by 91.2%. Furthermore, we implement a semi-supervised method using knowledge distillation and find that though it is outperformed by CheXseg, it exceeds the performance (mIoU) of the best fully-supervised method by 4.83%. Our best method is able to match radiologist agreement on three out of ten pathologies and reduces the overall performance gap by 71.6% as compared to weakly-supervised methods

CheXseen: Unseen Disease Detection for Deep Learning Interpretation of Chest X-rays

We systematically evaluate the performance of deep learning models in the presence of diseases not labeled for or present during training. First, we evaluate whether deep learning models trained on a subset of diseases (seen diseases) can detect the presence of any one of a larger set of diseases. We find that models tend to falsely classify diseases outside of the subset (unseen diseases) as "no disease". Second, we evaluate whether models trained on seen diseases can detect seen diseases when co-occurring with diseases outside the subset (unseen diseases). We find that models are still able to detect seen diseases even when co-occurring with unseen diseases. Third, we evaluate whether feature representations learned by models may be used to detect the presence of unseen diseases given a small labeled set of unseen diseases. We find that the penultimate layer of the deep neural network provides useful features for unseen disease detection. Our results can inform the safe clinical deployment of deep learning models trained on a non-exhaustive set of disease classes.Comment: Accepted to ACM Conference on Health, Inference, and Learning (ACM-CHIL) Workshop 202